def RecupererPattern(ident):
# la récupération des séquences à partir de la Base des données SwissProt
handle = ExPASy.get_prosite_raw(ident)
record = Prosite.read(handle)
if record.type == 'PATTERN':
return record.pattern
elif record.type == 'MATRIX':
print("L'identifiant que vous avez entré correspont à un profile !")
def __init__(self, s=None, ps=None):
if isinstance(s, basestring):
self.sequence = Seq(s)
else:
self.sequence = s
self.prosite = ExPASy.get_prosite_raw(ps)
self.record = Prosite.read(self.prosite)
self.pat = pa.compile(self.record.pattern)
self.regexp = re.compile(pa.prosite_to_re(self.record.pattern))
def RecupererPattern(ident):
handle = ExPASy.get_prosite_raw(ident)
record = Prosite.read(handle)
if record.type == 'PATTERN':
print("La forme régulière est: ", record.pattern)
print("La traduction en Python est: ",
traduireSequence(record.pattern))
elif record.type == 'MATRIX':
print("L'identifiant que vous avez entré correspont à un profile !")
def get_documentation(accession):
"""
get_documentation function gets as arg :
accesion (signature_ac example "PS00001" )
returns
html file containing full documentaion
"""
handle_1 = ExPASy.get_prosite_raw(accession)
records = Prosite.read(handle_1)
handle_2 = ExPASy.get_prodoc_entry(records.pdoc)
#record = Prodoc.read(handle_2)"
html = handle_2.read()
with open("my_prodoc_record.html", "w") as out_handle:
out_handle.write(html)
def Prosite_Domain(self):
from Bio import ExPASy
from Bio.ExPASy import Prosite, ScanProsite
try:
handle = ScanProsite.scan(seq=self.__seq_input)
result = ScanProsite.read(handle)
if len(result) != 0:
for res in range(len(result)):
prosite_acession = result[res]['signature_ac']
r = ExPASy.get_prosite_raw(prosite_acession)
html = Prosite.read(r)
r.close()
print('Foi encontrado um dominio %s.' % (html.name))
else:
print('Não foram encontradas correspondências.')
except:
print('A sequência fornecida não é uma sequência proteica.')
def test_prodoc_raw(self):
handle = ExPASy.get_prosite_raw("PDOC00001")
record = Prodoc.read(handle)
handle.close()
self.assertEqual(record.accession, "PDOC00001")
def test_prosite_raw(self):
handle = ExPASy.get_prosite_raw("PS00001")
record = Prosite.read(handle)
handle.close()
self.assertEqual(record.accession, "PS00001")
self.assertEqual(record.name, "ASN_GLYCOSYLATION")
def test_prodoc_raw(self):
handle = ExPASy.get_prosite_raw('PDOC00001')
record = Prodoc.read(handle)
handle.close()
self.assertEqual(record.accession, 'PDOC00001')
def test_prosite_raw(self):
handle = ExPASy.get_prosite_raw('PS00001')
record = Prosite.read(handle)
handle.close()
self.assertEqual(record.accession, 'PS00001')
self.assertEqual(record.name, 'ASN_GLYCOSYLATION')
def test_prodoc_raw(self):
with ExPASy.get_prosite_raw("PDOC00001") as handle:
record = Prodoc.read(handle)
self.assertEqual(record.accession, "PDOC00001")
def test_prosite_raw(self):
with ExPASy.get_prosite_raw("PS00001") as handle:
record = Prosite.read(handle)
self.assertEqual(record.accession, "PS00001")
self.assertEqual(record.name, "ASN_GLYCOSYLATION")
accessions = set()
motifs = ""
# Scan Prosite for matching motifs
handle = ScanProsite.scan(seq=sequence, skip="off")
result = ScanProsite.read(handle)
# Obtain all accession motifs
for hit in result:
acc = hit.get('signature_ac')
accessions.add(acc)
# Get descriptions from accession numbers
for accession in accessions:
prof = ExPASy.get_prosite_raw(accession)
text = prof.read()
text = text.splitlines()
desc = text[3]
desc = str.split(desc, 'DE ')
desc = desc[1]
desc = desc[0:(len(desc) - 1)]
motifs += desc + ";"
motifs = motifs[0:(len(motifs) - 1)]
motifset.append(motifs)
results = {"Name": input.iloc[:, 0], "Prosite": motifset}
output = pd.DataFrame(data=results)
from Bio import ExPASy
handle = ExPASy.get_prosite_raw("PS00001")
text = handle.read()
print(text)
# 가장 원시적인 긁는 방법 (Expasy만 있으면 됨)
"""from Bio import Prosite
handle = ExPASy.get_prosite_raw("PS51036")
record = Prosite.read(handle)
print(record)"""
# ImportError: cannot import name 'Prosite' from 'Bio' (/home/koreanraichu/PycharmProjects/pythonProject/venv/lib/python3.8/site-packages/Bio/__init__.py)가 나를 반기는디?
from Bio.ExPASy import Prodoc
handle = ExPASy.get_prosite_raw("PDOC00001")
record = Prodoc.read(handle)
print(record)
handle = ExPASy.get_prosite_entry("PS51036")
html = handle.read()
with open("myprositerecord.html", "w") as out_handle:
out_handle.write(html)
# HTML format으로 다운로드 받을 수 있다.
handle = ExPASy.get_prodoc_entry("PDOC51036")
html = handle.read()
with open("myprositerecord2.html", "w") as out_handle:
out_handle.write(html)
# 얘는 prodoc 다운로드 하는 코드
from Bio.ExPASy import ScanProsite, Prosite, Prodoc
from Bio import ExPASy
# 在线浏览蛋白质序列
sequence = "MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKCEEDEEFTCRAFQYHSKEQQCVIMAENRKSSIIIRMRDVVLFEKKVYLSECKTGNGKNYRGTMSKTKN"
handle = ScanProsite.scan(seq=sequence)
result = ScanProsite.read(handle)
print(result)
# 获取Prosite记录
handle = ExPASy.get_prosite_raw('PS00001')
record = Prosite.read(handle)
# record = Prodoc.read(handle)
print(record)
